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PLoS One. 2014 Jan 29;9(1):e86752. doi: 10.1371/journal.pone.0086752. eCollection 2014.

Genomic evolution of 11 type strains within family Planctomycetaceae.

Author information

1
Shenzhen Key Laboratory of Environmental Microbial Genomics and Application, BGI-Shenzhen, Shenzhen, China ; Shenzhen Key Laboratory of Bioenergy, BGI-Shenzhen, Shenzhen, China ; BGI-Shenzhen, Shenzhen, China.
2
BGI-Shenzhen, Shenzhen, China.
3
Shenzhen Key Laboratory of Bioenergy, BGI-Shenzhen, Shenzhen, China ; BGI-Shenzhen, Shenzhen, China.
4
Medical College, Nankai University, Tianjin, China.
5
Shenzhen Key Laboratory of Environmental Microbial Genomics and Application, BGI-Shenzhen, Shenzhen, China ; Shenzhen Key Laboratory of Bioenergy, BGI-Shenzhen, Shenzhen, China ; College of Life Sciences, Wuhan University, Wuhan, China.
6
Shenzhen Key Laboratory of Environmental Microbial Genomics and Application, BGI-Shenzhen, Shenzhen, China ; Shenzhen Key Laboratory of Bioenergy, BGI-Shenzhen, Shenzhen, China ; BGI-Shenzhen, Shenzhen, China ; State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.

Abstract

The species in family Planctomycetaceae are ideal groups for investigating the origin of eukaryotes. Their cells are divided by a lipidic intracytoplasmic membrane and they share a number of eukaryote-like molecular characteristics. However, their genomic structures, potential abilities, and evolutionary status are still unknown. In this study, we searched for common protein families and a core genome/pan genome based on 11 sequenced species in family Planctomycetaceae. Then, we constructed phylogenetic tree based on their 832 common protein families. We also annotated the 11 genomes using the Clusters of Orthologous Groups database. Moreover, we predicted and reconstructed their core/pan metabolic pathways using the KEGG (Kyoto Encyclopedia of Genes and Genomes) orthology system. Subsequently, we identified genomic islands (GIs) and structural variations (SVs) among the five complete genomes and we specifically investigated the integration of two Planctomycetaceae plasmids in all 11 genomes. The results indicate that Planctomycetaceae species share diverse genomic variations and unique genomic characteristics, as well as have huge potential for human applications.

PMID:
24489782
PMCID:
PMC3906078
DOI:
10.1371/journal.pone.0086752
[Indexed for MEDLINE]
Free PMC Article

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